Installing RFantibody on HPC cluster without root access (no Docker)

[mehedihasandesu]

Hi RFantibody team / community,

I am trying to install RFantibody on an HPC cluster where I do not have root access. Could you please advise on the best approach in this situation?

Specifically:
Is it possible to install and run RFantibody without using Docker?
Alternatively, is there a way to use Docker (or an equivalent container runtime) without root privileges?

Any guidance or recommended setup for this would be greatly appreciated.

Thanks!

Mehedi Hasan

[JPayr]

I had the same issue and have managed to get around it by using apptainer

[aspitaleri]

What about #32 ?
https://github.com/hegelab/RFantibody/tree/singularity-and-fixes it should work

[Apatura-iris1]

I managed to run RFantibody on our HPC without root access by:

1. Set up local conda environments and install dependencies.
2. Install RFantibody inside cloned repo (pip install -e).
3. Ensure python path is correct (e.g. PYTHONPATH=$PWD/src/rfantibody/rfdiffusion:$PYTHONPATH)

This works fully without docker or apptainer.

[aspitaleri]

@Apatura-iris1 which dependencies on conda env? I could not find it (a part docker binary). These could be:
https://github.com/RosettaCommons/RFantibody/blob/main/pyproject.toml

[aspitaleri]

I did as suggested in https://github.com/hegelab/RFantibody/tree/singularity-and-fixes:

git clone --branch main https://github.com/hegelab/RFantibody.git
cd RFantibody
bash include/download_weights.sh
singularity build --fakeroot RFantibody_base.sif singularity.def
singularity shell --nv --no-home -B $(pwd):/opt/RFantibody RFantibody_base.sif
(Singularity)$ cd $HOME
(Singularity)$ bash include/setup_sif.sh
(Singularity)$ exit

that's it

[Apatura-iris1]

Yeah I built the conda env manually by looking through all the setup scripts.

I kept having issues with apptainer and rebuilding obviously require root access hence using conda.

If anyone has issues I can find my requirements.txt

[ppxwwtaking]

Yeah I built the conda env manually by looking through all the setup scripts.

I kept having issues with apptainer and rebuilding obviously require root access hence using conda.

If anyone has issues I can find my requirements.txt

Do you mind if you can upload the conda env file?

[Apatura-iris1]

Here's what I used, please note I NVIDIA GPU and CUDA 11.8 runtime.

torch==2.3.*
torchvision==0.18.*
torchaudio==2.3.*
numpy==1.*
cuda-python==11.8.*
hydra-core
icecream
opt-einsum
e3nn
pyrsistent
dgl-cu118